From c822f8b98d6eadac867e77919d3bb82e545e6fb4 Mon Sep 17 00:00:00 2001
From: Sam Yates <yates@cscs.ch>
Date: Mon, 15 Oct 2018 15:49:35 +0200
Subject: [PATCH] Patch up Julia scripts for Julia 1.0 (#629)
* Use `Unitful.uconvert` for scalar conversions (Float64 cast apparently does not work at the moment).
* Use .+ for scalar/array addition.
* Replace `immutable` with `struct`.
* Qualify included modules with `Main.` for using statements.
* Add informational note to FindJulia as component identification can take a long time as Julia may compile them from source.
---
cmake/FindJulia.cmake | 3 +++
validation/ref/numeric/HHChannels.jl | 5 ++---
validation/ref/numeric/LVAChannels.jl | 4 ++--
validation/ref/numeric/PassiveCable.jl | 4 +++-
validation/ref/numeric/numeric_kin1.jl | 2 +-
validation/ref/numeric/numeric_kinlva.jl | 2 +-
validation/ref/numeric/numeric_rallpack1.jl | 2 +-
validation/ref/numeric/numeric_soma.jl | 2 +-
8 files changed, 14 insertions(+), 10 deletions(-)
diff --git a/cmake/FindJulia.cmake b/cmake/FindJulia.cmake
index b9c91377..b6ce48dd 100644
--- a/cmake/FindJulia.cmake
+++ b/cmake/FindJulia.cmake
@@ -14,6 +14,9 @@ include(FindPackageHandleStandardArgs)
if(NOT Julia_FOUND)
find_program(Julia_EXECUTABLE julia)
if(Julia_EXECUTABLE)
+ if(Julia_FIND_COMPONENTS)
+ message(STATUS "Checking for Julia components: ${Julia_FIND_COMPONENTS}")
+ endif()
foreach(component ${Julia_FIND_COMPONENTS})
set(_found_var "Julia_${component}_FOUND")
if(NOT ${_found_var})
diff --git a/validation/ref/numeric/HHChannels.jl b/validation/ref/numeric/HHChannels.jl
index f68a7aa1..317b8d76 100644
--- a/validation/ref/numeric/HHChannels.jl
+++ b/validation/ref/numeric/HHChannels.jl
@@ -6,7 +6,7 @@ using Sundials
using Unitful
using Unitful.DefaultSymbols
-immutable HHParam
+struct HHParam
c_m # membrane spacific capacitance
gnabar # Na channel cross-membrane conductivity
gkbar # K channel cross-membrane conductivity
@@ -47,7 +47,7 @@ immutable HHParam
end
-immutable Stim
+struct Stim
t0 # start time of stimulus
t1 # stop time of stimulus
i_e # stimulus current density
@@ -144,7 +144,6 @@ function run_hh(t_end; v0=-65mV, stim=Stim(), param=HHParam(), sample_dt=0.01ms)
ydot[1], ydot[2], ydot[3], ydot[4] =
vdot*t_scale/v_scale, mdot*t_scale, hdot*t_scale, ndot*t_scale
-# Float64(vdot*t_scale/v_scale), Float64(mdot*t_scale), Float64(hdot*t_scale), Float64(ndot*t_scale)
return Sundials.CV_SUCCESS
end
diff --git a/validation/ref/numeric/LVAChannels.jl b/validation/ref/numeric/LVAChannels.jl
index a1f4e865..46ec1cd3 100644
--- a/validation/ref/numeric/LVAChannels.jl
+++ b/validation/ref/numeric/LVAChannels.jl
@@ -6,7 +6,7 @@ using Sundials
using Unitful
using Unitful.DefaultSymbols
-immutable LVAParam
+struct LVAParam
c_m # membrane spacific capacitance
gbar # Ca channel cross-membrane conductivity
eca # Ca channel reversal potential
@@ -32,7 +32,7 @@ immutable LVAParam
end
-immutable Stim
+struct Stim
t0 # start time of stimulus
t1 # stop time of stimulus
i_e # stimulus current density
diff --git a/validation/ref/numeric/PassiveCable.jl b/validation/ref/numeric/PassiveCable.jl
index 56eded5a..9f5858bf 100644
--- a/validation/ref/numeric/PassiveCable.jl
+++ b/validation/ref/numeric/PassiveCable.jl
@@ -1,5 +1,7 @@
module PassiveCable
+using Unitful: uconvert, NoUnits
+
export cable_normalize, cable, rallpack1
# Compute solution g(x, t) to
@@ -94,7 +96,7 @@ function cable(x, t, L, lambda, tau, r, V, I; tol=1e-8)
return V
else
tol_n = abs(tol/scale)
- return scale*cable_normalized(Float64(x/lambda), Float64(t/tau), Float64(L/lambda), tol=tol_n) + V
+ return scale*cable_normalized(uconvert(NoUnits, x/lambda), uconvert(NoUnits, t/tau), uconvert(NoUnits, L/lambda), tol=tol_n) + V
end
end
diff --git a/validation/ref/numeric/numeric_kin1.jl b/validation/ref/numeric/numeric_kin1.jl
index 4437c3c8..42508dc9 100644
--- a/validation/ref/numeric/numeric_kin1.jl
+++ b/validation/ref/numeric/numeric_kin1.jl
@@ -19,7 +19,7 @@ c = 0.01mA/cm^2
tau = 10ms
ts = collect(0s: sample_dt: t_end)
-is = area*(1/3*c + (a0-1/3*c)*exp.(-ts/tau))
+is = area*(1/3*c .+ (a0-1/3*c)*exp.(-ts/tau))
trace = Dict(
:name => "membrane current",
diff --git a/validation/ref/numeric/numeric_kinlva.jl b/validation/ref/numeric/numeric_kinlva.jl
index 108612e7..55bf6773 100644
--- a/validation/ref/numeric/numeric_kinlva.jl
+++ b/validation/ref/numeric/numeric_kinlva.jl
@@ -5,7 +5,7 @@ include("LVAChannels.jl")
using JSON
using Unitful
using Unitful.DefaultSymbols
-using LVAChannels
+using Main.LVAChannels
scale(quantity, unit) = uconvert(NoUnits, quantity/unit)
diff --git a/validation/ref/numeric/numeric_rallpack1.jl b/validation/ref/numeric/numeric_rallpack1.jl
index 9830d81c..41c54f80 100644
--- a/validation/ref/numeric/numeric_rallpack1.jl
+++ b/validation/ref/numeric/numeric_rallpack1.jl
@@ -5,7 +5,7 @@ include("PassiveCable.jl")
using JSON
using Unitful
using Unitful.DefaultSymbols
-using PassiveCable
+using Main.PassiveCable
scale(quantity, unit) = uconvert(NoUnits, quantity/unit)
diff --git a/validation/ref/numeric/numeric_soma.jl b/validation/ref/numeric/numeric_soma.jl
index 7c5e1336..36370b2e 100644
--- a/validation/ref/numeric/numeric_soma.jl
+++ b/validation/ref/numeric/numeric_soma.jl
@@ -5,7 +5,7 @@ include("HHChannels.jl")
using JSON
using Unitful
using Unitful.DefaultSymbols
-using HHChannels
+using Main.HHChannels
scale(quantity, unit) = uconvert(NoUnits, quantity/unit)
--
GitLab